Regarding the game I'm playing is Kingdom Hearts 2 final mix, and I love the game and all and it works great on the emulator, the framerate is capped at 60, and the game is always dipping under that either by .5 frames or even 5 frames. This is very very small, but the problem being that this is constant, I can both see and feel it. My monitor refresh rate is 60hz, so if I can cap the fps at 80 that would be awesome.

I messed around with the settings myself, and I got the game to run at around 300 fps but the speed went up to 150 - 200%. I don't want that, is there a way to increase the framerate cap without making the game faster, just keep it at 100% / normal speed.

The FPS counter you see in the title bar in the emulator is less FPS and more a speed measure. For NTSC regions, the PS2 output at 59.94 FPS, PAL regions 50 FPS. This was the final output actually being sent to the TV, and in the case of PCSX2 emulating that output to your screen, that's the measurable value that we can display. The internal framerate is much harder to do because of the PS2's rather complicated GS, and it just simply hasn't been done yet.

My point with all this is, if you try disabling the frame limiter, the game will speed up. Period. You aren't unbinding the internal frame limiter, you're unbinding the entire system so it will run as fast as possible in every regard. If you simply want an internal FPS boost, you can try increasing the EE cyclerate a tick or two, but note this may or may not have much effect, and can increase CPU requirements a good amount.